Healthy building design is an emerging field of architecture and building engineering. Indoor air quality (IAQ) is an inevitable factor that should be considered in healthy building design due to its demonstrated links with human health and well-being. This paper proposes to integrate IAQ prediction into healthy building design by developing a simulation toolbox, termed i-IAQ, using MATLAB App Designer. Within the i-IAQ, users can input information of building layout and wall-openings and select air pollutant sources from the database. As an output, the toolbox simulates indoor levels of carbon dioxide (CO2), total volatile organic compounds (TVOC), inhalable particles (PM10), fine particles (PM2.5), nitrogen dioxide (NO2), and ozone (O-3) during the occupied periods. Based on the simulation results, the toolbox also offers diagnosis and recommendations to improve the design. The accuracy of the toolbox was validated by a case study in an apartment where physical measurements of air pollutants took place. The results suggest that designers can integrate the i-IAQ toolbox in building design, so that the potential IAQ issues can be resolved at the early design stage at a low cost. The paper outcomes have the potential to pave a way towards more holistic healthy building design, and novel and cost-effective IAQ management.